Microbiota and metabolome dynamics induced by Shiga toxin-producing E. coli in an in vitro model of an infant’s colon

Shiga toxin-producing Escherichia coli (STEC) is a major food-borne pathogen causing human diseases ranging from diarrhea to life-threatening complications, mainly in young children. Colonization, virulence, and interactions of STEC strains with human gut microbiota are pivotal during infection but remain poorly described, particularly in children, the most affected population. In this work, we evaluated changes in the microbiota and metabolome composition in the <i>in vitro</i> gut model: Toddler ARtificial COLon (T-ARCOL) infected with EHEC O157:H7 strain EDL 933. Stool samples collected from children with STEC-positive diarrhea and stool from the same children after recovery from the diarrheal episode (<i>n=5</i>) were used to inoculate the T-ARCOL model. STEC colonization was progressively reduced throughout fermentation in T-ARCOL with diarrhea or recovery fecal samples. Beta diversity showed that the diarrhea-associated microbiota was significantly distinct from the recovery microbiota and exhibited a lower α-diversity. In contrast to recovery conditions, diarrheal conditions were characterized by an increased abundance of potential pathobionts such as members of the <i>Clostridiaceae</i> family and higher acetate, succinate, and N-acetylneuraminic acid levels. Our results provide new evidence of the impact of EHEC in the microbiota and metabolome dynamics in an in vitro gut model that could be useful in understanding their physiopathology in this at-risk population, considering inter-individual variabilities in gut microbiota.